There are some differences in the 2.5 blocks, but those may just be differences between the XJ 2.5 and Wrangler engines. My 1984 XJ 2.5 was a bit different than the '93 YJ 2.5. Intake and exhaust patterns, engine mounts, and bellhousing are identical, though.
-'84-'85 use smaller diameter head bolts
-somewhere around 1990 the valve spring retainers shrunk in size, tapered (beehive) springs replaced the old straight ones, and the keepers went 3-groove instead of 1.
-the XJ timing cover has some small differences in bolt pattern where the alternator brackets mount.
-the XJ 2.5 crank is longer at the harmonic balancer, and belt alignment is about 1/4" further from the block than the YJ.
-the early years had a fuel pump mount/hole in the the block, the later years have this blocked out and it is just a coil mount.
-though the oil pans are identical, the later model oil pan gaskets are reusable rubber, and seal way better.